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How could I analyse the differential expression of a particular gene with RNA-seq data?

Hi everyone! I'm new in RNA-seq data analysis. I'm interested in the differential analysis of a set of particular genes from an open access raw data. So I want to know which tools I need to use, specially after the mapping. So please help me I'm confuse.

rna-seq gene
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updated by swbarnes2 swbarnes2 • written by bioAddict • bioAddict

Read the edgeR Userguide. It's a good discussion of many of the issues involved, has discussions of experimental designs, a section on gene set testing, and is very accessible.

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written by seidel seidel

1 answer

Use RSEM to count genes, then use DESeq2 or EdgeR. Of course, you have to process the whole dataset, not just your favorite subset.

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written by swbarnes2 swbarnes2

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